Was he just in killing off a bunch of brain-sucked victims so there's no chance ever that anyone could reverse their brain suck? No. It's not clear what happened to those that survived but Ben was not god, even if he lived inside one.
Was he justified in siding with Glory? Of course not. I feel sorry for him, but the honourable choice is to do that which will result in the fewest fatalities. His choice to cooperate with Glory could not fail to result in more human misery. If you have to let the train run over one person, even if that person is you, in order to prevent derailment... that kills all the people on the train, and maybe causes damage to the surrounding people? There's only one moral choice. Is it a fun choice? heck no.
We cannot justify malign actions because they serve OUR needs. If the politicians would learn this, our planet would be in far better shape... but that's off topic.
Honourable action would have been suicide. He had access to all sorts of meds. If one doesn't care about being caught, it's easy to get meds in a hospital. Even air in the veins. Once he could sense who she was, he had a choice. even before that, he knew what she was doing. He knew he couldn't survive. He was simply wanting to live more than the earth and all other dimensions. Not much of a prize, Ben.